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mmu_circSsx2ip_281
Basic information of circular RNA
PanCircBase ID:
mmu_circSsx2ip_281
mm39_Chr. Position ID:
chr3|146142297|146143096|+
Gene name:
Ssx2ip
Transcript:
ENSMUST00000106151.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
12,13
Exon/intron offsets:
0,633
Genomic length:
799
Exon/intron sizes in nt:
115,166
Flanking exon/introns:
chr3:146138901-146142297|chr3:146143096-146144410
Splice length:
281
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGAAAGGCGTTTGAAGAAGAGCGAGCCAGCTGGGTAAAGCAGCAGTTTTTAAACATGACGAACTTTGACCACCAGAACTCAGAAAATGTGAAACTTTTCAGTGCCTTCTCAGGAAGTTCTGATCCAGACAATCTTATAGTCCACTCACGGCCACGGCAAAAGAAGCTACACAGTGTGGCTAATGGGGTGCCAGCTTGCACATCAAAACTGACTAAATCTCTTCCTGCCTCACCTTCTACTTCAGACTTTCGCCAGACACATTCATGTGTGTCTGAACACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCAGCTTGCACATCAAAA
59.25
TCTGGTGGTCAAAGTTCGTCA
59.52
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAGCTTGCACATCAAAAC
58.86
TCTGGTGGTCAAAGTTCGTCA
59.52
169
PCR template sequence:
ATGGGGTGCCAGCTTGCACATCAAAACTGACTAAATCTCTTCCTGCCTCACCTTCTACTTCAGACTTTCGCCAGACACATTCATGTGTGTCTGAACACAGAGAAAGGCGTTTGAAGAAGAGCGAGCCAGCTGGGTAAAGCAGCAGTTTTTAAACATGACGAACTTTGACCACCAGAACTCAGAAAATGTGAAACTTTTCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-23b-3p(1), mmu-let-7e-5p(1), mmu-miR-23a-3p(1), mmu-miR-149-5p(1), mmu-miR-383-5p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCTGAACACAGAGAAAGGCGTTTG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSSX2IP_281_ORF_1
0.6854
0.040325789
0.128790799
264
ORF sequence:
ATGACGAACTTTGACCACCAGAACTCAGAAAATGTGAAACTTTTCAGTGCCTTCTCAGGAAGTTCTGATCCAGACAATCTTATAGTCCACTCACGGCCACGGCAAAAGAAGCTACACAGTGTGGCTAATGGGGTGCCAGCTTGCACATCAAAACTGACTAAATCTCTTCCTGCCTCACCTTCTACTTCAGACTTTCGCCAGACACATTCATGTGTGTCTGAACACAGAGAAAGGCGTTTGAAGAAGAGCGAGCCAGCTGGGTAA
Peptide sequence:
MTNFDHQNSENVKLFSAFSGSSDPDNLIVHSRPRQKKLHSVANGVPACTSKLTKSLPASPSTSDFRQTHSCVSEHRERRLKKSEPAG
IRESfinder result
IRESfinder score
0.656675206
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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